16
+ − 1 <tool id="SAPP_genome_to_ttl" name="FASTA to RDF" version="0.1">
+ − 2 <requirements>
+ − 3 <requirement type='package' version="3.4">python</requirement>
+ − 4 <requirement type='package' version="1.0">rdflib</requirement>
+ − 5 </requirements>
+ − 6 <description></description>
+ − 7 <command interpreter="python3">fastatordf.py '-input' '$input' '-output' '$output' '-organism' '$organism' '-ncbi_taxid' '$ncbi_taxid' '-idtag' '$identification_tag' -sourcedb SAPP
+ − 8 #for $index, $id in enumerate( $ids )
+ − 9 '-ids' '$id.id_tag'
+ − 10 #end for
+ − 11 '-id_alternative' '$input.name'
+ − 12 </command>
+ − 13 <inputs>
+ − 14 <param size="60" name="input" type="data" format="fasta,fa" label="File for annotation, file types used fasta,fa"/>
+ − 15 <param size="60" name="organism" type="text" format="text" label="organism name" optional="false"/>
+ − 16 <param size="60" name="ncbi_taxid" type="text" format="text" label="NCBI taxonomy ID"/>
+ − 17 <param size="60" name="identification_tag" type="text" format="text" label="An identification tag used for RDF storage !Needs to be very unique!" optional="false"/>
+ − 18 <repeat name="ids" title="Identification tags">
+ − 19 <param size="60" name="id_tag" type="text" format="text" label="An identification tag used by other consortiums"/>
+ − 20 </repeat>
+ − 21 </inputs>
+ − 22
+ − 23 <outputs>
+ − 24 <data format="rdf" name="output" label="genomeTTL: ${input.name}" />
+ − 25 </outputs>
+ − 26
+ − 27 <tests>
+ − 28 <test>
+ − 29 <param name="input" value="test-data/NC_017117.fna"/>
+ − 30 <output name="$output" file="NC_017117.rdf"/>
+ − 31 <output name="$ncbi_taxid" value="634455"/>
+ − 32 <output name="$idtag" value="Acetobacter pasteurianus IFO 3283-22"/>
+ − 33 <output name="$organism" value="Acetobacter pasteurianus IFO 3283-22"/>
+ − 34 </test>
+ − 35 </tests>
+ − 36
+ − 37 <help> Genome FASTA file to RDF</help>
+ − 38 </tool>